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pubmed-mcp-server

by io.github.cyanheads

Pubmed Find Related

pubmed_find_related
Read-only

Find articles related to a source article — similar content (similar), articles citing this one (cited_by), or articles this one cites (references). Uses NCBI ELink as the primary source; falls back to Europe PMC then OpenAlex when NCBI is unavailable.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidYesSource PubMed ID
offsetNoResult offset for pagination (0-based); page through results by incrementing by maxResults
maxResultsNoMaximum related articles
relationshipNoRelationship type: similar (content-based), cited_by (articles citing this one), references (articles this one cites)similar

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
noticeNoGuidance when results are empty, a fallback provider answered, or offset overshot. Absent on a clean NCBI result page.
offsetNoResult offset used
sourceNoProvider that answered this request
articlesNoRelated articles
sourcePmidNoSource PubMed ID
totalCountNoTotal related articles found before windowing
relationshipNoRelationship type used

TDQS

A4.2/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Beyond the readOnlyHint and openWorldHint annotations, the description discloses the fallback mechanism (NCBI ELink → Europe PMC → OpenAlex) and the nature of the relationships. This adds behavioral context not present in the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, concise sentence that front-loads the primary action and purpose, then adds the relationship options and fallback details. It is efficient and well-structured.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the presence of an output schema and annotations, the description adequately covers the tool's purpose and behavior. It could mention output shape or limitations, but the fallback details and relationship types provide sufficient context for correct usage.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Parameter descriptions in the schema already cover pmid, offset, maxResults, and relationship (including enum values). The tool description repeats the relationship enum meanings without adding new constraints or examples, so it provides marginal additional value beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose: finding articles related to a source article, with specific relationship types (similar, cited_by, references). It distinguishes itself from sibling tools like search and fetch by focusing on relatedness, and the mention of fallback sources adds specificity.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for retrieving related articles, which is distinct from searching or fetching. However, it does not explicitly state when this tool should be preferred over siblings or when it is inappropriate to use, leaving some ambiguity for an agent.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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TDQS

A4.2/5.0
Disambiguation4/5

The tools constitute a well-designed set targeting distinct workflow steps: searching (pubmed_search_articles, pubmed_europepmc_search), fetching (pubmed_fetch_articles, pubmed_fetch_fulltext, pubmed_europepmc_fetch), ID conversion (pubmed_convert_ids), related articles (pubmed_find_related), citations (pubmed_format_citations, pubmed_lookup_citation), MeSH lookup (pubmed_lookup_mesh), and spelling (pubmed_spell_check). While search and fetch tools in PubMed vs Europe PMC overlap somewhat, the descriptions explicitly differentiate them (local PubMed vs broader Europe PMC with preprints/patents), so ambiguity is minor.

Naming Consistency5/5

All tools follow a consistent `pubmed_` prefix followed by verb_noun pattern: `search_articles`, `fetch_articles`, `lookup_citation`, `format_citations`, `convert_ids`, `find_related`, etc. The verbs are all lowercase snake_case, and the pattern is uniform across the entire set, even for the Europe PMC variants (`pubmed_europepmc_search`, `pubmed_europepmc_fetch`).

Tool Count5/5

11 tools makes for a well-scoped server. Each tool serves a clearly distinct purpose within the biomedical literature retrieval domain: searching, fetching metadata/full-text, ID conversion, citation formatting/lookup, MeSH exploration, related-articles, and spell-check. No tool feels redundant or trivial; the count is appropriate for the domain's complexity.

Completeness5/5

The tool set provides comprehensive coverage of the core PubMed/PMC workflow: search with full query syntax, fetch metadata and full text, convert identifiers across DOI/PMID/PMCID, find related articles, format citations, and explore MeSH vocabulary. Notable gaps like more advanced search history management or batch operations exist but are not essential to the domain's core purpose. The fallback logic (e.g., europepmc_fetch for non-PMC records, fulltext fallback chain) fills potential dead ends.

Resources